Orthofinder
Description
OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.
License
GNU GPL v3, https://www.gnu.org/copyleft/gpl.html
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of orthofinder and load default version of orthofinder as
module avail orthofinder/ # list available modules module load orthofinder # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail orthofinder
and choose explicit version you want to use.
Documentation
Official website: https://github.com/davidemms/OrthoFinder
Official documentation: https://github.com/davidemms/OrthoFinder#running-orthofinder
Original paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0721-2